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Computational Radiomics System to Decode the Radiographic Phenotype

Presents PyRadiomics, an open-source Python platform extracting a large panel of engineered radiomic features from medical images to standardize analyses.

Radiomics quantifies phenotypic traits on medical imaging using automated algorithms, enabling non-invasive biomarkers, but a lack of standardized algorithm definitions and image processing hampers reproducibility. To address this, the authors built PyRadiomics, a flexible open-source platform that extracts a large panel of engineered features from medical images. Implemented in Python, it runs standalone or via 3D-Slicer. The paper describes its architecture and demonstrates it on lung-lesion characterization, aiming to set a reference standard.

Based on: Computational Radiomics System to Decode the Radiographic Phenotype · Cancer Research

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Fundamentals of Recurrent Neural Network (RNN) and Long Short-Term Memory (LSTM) Network

A tutorial that formally derives RNN and LSTM equations from differential equations, justifies unrolling, and proposes a generalized Vanilla LSTM.

LSTM networks are widely covered, but most articles state inference formulas axiomatically, omit training formulas, and present RNN 'unrolling' without justification. This tutorial explains essential RNN and LSTM fundamentals in one document. Drawing on signal processing, it formally derives the canonical RNN from differential equations and proves a statement yielding the unrolling technique. It then transforms the RNN into a Vanilla LSTM through logical arguments, provides all governing equations, and introduces extensions producing the most general LSTM variant to date.

Based on: Fundamentals of Recurrent Neural Network (RNN) and Long Short-Term Memory (LSTM) Network · Physica A: Statistical Mechanics and its Applications

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Long-term recurrent convolutional networks for visual recognition and description

Introduces LRCN, an end-to-end recurrent convolutional architecture uniting CNNs and RNNs for video recognition, captioning, and narration.

This work asks whether recurrent, 'temporally deep' models help on sequential tasks such as video. It develops a novel, end-to-end trainable recurrent convolutional architecture and demonstrates it on video recognition, image description and retrieval, and video narration. Unlike models with a fixed spatio-temporal receptive field or simple temporal averaging, these 'doubly deep' models are compositional in space and time, map variable-length inputs to variable-length outputs, and train via backpropagation while jointly learning temporal dynamics and visual representations.

Based on: Long-term recurrent convolutional networks for visual recognition and description · Computer Vision and Pattern Recognition

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An experimental comparison of min-cut/max- flow algorithms for energy minimization in vision

Experimentally compares min-cut/max-flow algorithms for energy minimization in vision, introducing a new method often several times faster than others.

Min-cut/max-flow algorithms have become useful tools for energy minimization in low-level vision, but their practical efficiency had mostly been studied outside computer vision. This paper experimentally compares running times of several standard algorithms—including Goldberg-Tarjan push-relabel and Ford-Fulkerson augmenting-paths methods—plus a new algorithm the authors developed. Benchmarks span image restoration, stereo, and segmentation. In many cases the new algorithm runs several times faster, enabling near real-time performance.

Based on: An experimental comparison of min-cut/max- flow algorithms for energy minimization in vision · IEEE Transactions on Pattern Analysis and Machine Intelligence

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Bag of Tricks for Efficient Text Classification

Presents fastText, a simple, fast text-classification baseline that rivals deep learning accuracy while training orders of magnitude faster on CPU.

This paper explores a simple and efficient baseline for text classification. The authors' fast classifier, fastText, is often on par with deep learning classifiers in accuracy while being many orders of magnitude faster to train and evaluate. It can be trained on more than one billion words in under ten minutes using a standard multicore CPU, and can classify half a million sentences among 312K classes in less than a minute.

Based on: Bag of Tricks for Efficient Text Classification · Conference of the European Chapter of the Association for Computational Linguistics

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The MR-Base platform supports systematic causal inference across the human phenome

Introduces MR-Base, a platform pairing a curated GWAS database with software that automates 2-sample Mendelian randomization for causal inference.

GWAS results can infer causal relationships between phenotypes via 2-sample Mendelian randomization (2SMR) without individual-level data, but rapidly evolving methods and poorly curated data hinder implementation. MR-Base integrates a curated database of complete GWAS results with an API, web app, and R packages that automate 2SMR, plus sensitivity analyses for horizontal pleiotropy. The database holds 11 billion SNP-trait associations from 1673 GWAS and is regularly updated, letting millions of potential causal relationships be evaluated in phenome-wide studies.

Based on: The MR-Base platform supports systematic causal inference across the human phenome · eLife

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Review of deep learning: concepts, CNN architectures, challenges, applications, future directions

A comprehensive survey of deep learning: concepts, CNN architectures from AlexNet to HRNet, challenges, applications, and future directions.

This review offers a holistic survey of deep learning (DL), the dominant machine learning paradigm, which matches or exceeds human performance on many complex tasks across domains like cybersecurity, NLP, bioinformatics, and robotics. Noting that prior reviews each covered only one aspect, it presents DL's importance, its techniques and network types, and focuses on convolutional neural networks (CNNs), tracing architectures from AlexNet to the High-Resolution network (HRNet). It also covers challenges and solutions, applications, computational tools (FPGA, GPU, CPU), and benchmark datasets.

Based on: Review of deep learning: concepts, CNN architectures, challenges, applications, future directions · Journal of Big Data

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Least Squares Generative Adversarial Networks

Introduces Least Squares GANs, which use a least squares discriminator loss to improve image quality and stabilize GAN training.

Regular GANs treat the discriminator as a classifier with a sigmoid cross-entropy loss, which the authors show can cause vanishing gradients. This paper proposes Least Squares GANs (LSGANs), which adopt a least squares loss for the discriminator. Minimizing the LSGAN objective corresponds to minimizing the Pearson chi-square divergence. LSGANs generate higher quality images and train more stably. Experiments on LSUN and CIFAR-10 show better image quality than regular GANs, and comparisons illustrate improved stability.

Based on: Least Squares Generative Adversarial Networks · IEEE International Conference on Computer Vision

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Isogeometric analysis : CAD, finite elements, NURBS, exact geometry and mesh refinement

Proposes isogeometric analysis, using NURBS basis functions to unify exact CAD geometry with finite element analysis and mesh refinement.

The paper proposes isogeometric analysis, in which basis functions from NURBS (Non-Uniform Rational B-Splines) construct an exact geometric model. For analysis, the basis is refined or order-elevated without changing the geometry, giving analogues of finite element h- and p-refinement plus a new, more efficient higher-order k-refinement. Exact geometry is maintained without further CAD communication. Numerical examples show optimal convergence for linear elasticity, convergence to thin elastic shells, and monotone behavior for advection-diffusion with sharp layers.

Based on: Isogeometric analysis : CAD, finite elements, NURBS, exact geometry and mesh refinement · Semantic Scholar

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Spectral Networks and Locally Connected Networks on Graphs

Generalizes CNNs to graphs via hierarchical clustering and the graph Laplacian spectrum, learning convolutions independent of input size.

Convolutional neural networks are highly efficient for image and audio recognition because they exploit the local translational invariance of signals. This paper explores generalizing CNNs to signals defined on general domains lacking a translation group. It proposes two constructions: one based on hierarchical clustering of the domain, another on the spectrum of the graph Laplacian. Experiments show that for low-dimensional graphs, convolutional layers can be learned with parameters independent of input size, yielding efficient deep architectures.

Based on: Spectral Networks and Locally Connected Networks on Graphs · International Conference on Learning Representations

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Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning

Studies CNN architectures, dataset scale, and ImageNet transfer learning for medical computer-aided detection of lymph nodes and lung disease.

Deep CNNs excel at image recognition given large annotated datasets, but such data is scarce in medical imaging. This paper examines three understudied factors for applying CNNs to computer-aided detection: architecture, dataset scale and spatial context, and when ImageNet transfer learning helps. Models range from 5 thousand to 160 million parameters. Studying lymph node detection and interstitial lung disease classification, the authors reach state-of-the-art mediastinal lymph node detection and report first five-fold cross-validation results for ILD.

Based on: Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning · IEEE Transactions on Medical Imaging

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Heart Disease and Stroke Statistics—2015 Update: A Report From the American Heart Association

Describes STRIDE, a standards-based clinical informatics platform with a data warehouse, app framework, and biospecimen management.

STRIDE (Stanford Translational Research Integrated Database Environment) is a Stanford project building a standards-based informatics platform for clinical and translational research. It has three parts: a clinical data warehouse based on the HL7 Reference Information Model, holding data on over 1.3 million patients treated at Stanford since 1995; an app development framework for research data; and a biospecimen management system. Its semantic model uses standardized terminologies like SNOMED, RxNorm, ICD, and CPT, supporting Stanford's CTSA Informatics Program.

Based on: Heart Disease and Stroke Statistics—2015 Update: A Report From the American Heart Association · Circulation

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